rs1426745

Variant names:

• chr17-55699134-A-G
• rs1426745

Your query was ambiguous. Multiple possible variants found:

• chr17-55699134-A-G
• chr17-55699134-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.384 in 152,040 control chromosomes in the GnomAD database, including 17,048 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (17048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58296 AN: 151922 Hom.: 16999 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.372

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.384 AC: 58394 AN: 152040 Hom.: 17048 Cov.: 32 AF XY: 0.380 AC XY: 28255 AN XY: 74334

African (AFR) AF: 0.798 AC: 33119 AN: 41490

American (AMR) AF: 0.463 AC: 7072 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2307 AN: 5150

South Asian (SAS) AF: 0.227 AC: 1093 AN: 4820

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10600

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11626 AN: 67946

Other (OTH) AF: 0.368 AC: 775 AN: 2104

Alfa AF: 0.262 Hom.: 9958

Bravo AF: 0.432

Asia WGS AF: 0.361 AC: 1253 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	18
DANN	Benign	0.57
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1426745; hg19: chr17-53776495;